I use a machinist's level to do the base board first, make sure it is as perfect as you can make it. Any level will work (a small yard sale "torpedo level" is very good), just make sure you use the same edge facing up each time. Shims can be paper strips, tape, plywood or (worst case scenario) bricks. Once this is done, the negative stage is what needs to be perfect also. This is sometimes a bit more difficult. Use adjustments carefully and again, keep the same side of the level up like you did the first time. I've seen people use a cigarette, ball bearing or cup of water to do the test for flat and level. Remember, you just want the base board parallel to the negative.
First, make a print to see if one edge or side is out of focus. If it works well, leave it alone! Don't start adjusting anything until you know there is a problem. You may find that there is no reason to adjust it.